suppressMessages(library(ArchR))
library(parallel)
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=11, repr.plot.height=8.5)
##################################
### set Arrow File parameters ####
addArchRThreads(threads = round(parallel::detectCores()*1/4))
# ##################################
# ### load rheMac10 ArchR genome ###
# GENOMEDIR='/home/bnphan/resources/genomes/rheMac10'
# load(file.path(GENOMEDIR,'rheMac10_liftoff_GRCh38.p13_ArchR_annotations.rda'))
addArchRGenome("mm10")
Setting default number of Parallel threads to 8. Setting default genome to Mm10.
PROJDIR='../../../data/tidy_data/ArchRProjects'
ARCHDIR=file.path(PROJDIR,'Mouse_DorsalHorn_scATAC')
proj = loadArchRProject(ARCHDIR)
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
head(getCellColData(proj))
DataFrame with 6 rows and 24 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG Mouse_DH_SEA2253A58 14.994
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT Mouse_DH_SEA2253A58 22.800
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA Mouse_DH_SEA2253A58 21.583
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA Mouse_DH_SEA2253A58 22.169
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC Mouse_DH_SEA2253A58 19.802
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC Mouse_DH_SEA2253A58 20.646
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG 9268 32448
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT 14496 48252
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA 14442 47003
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA 14095 47225
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC 12110 40594
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC 12626 42748
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG 4805 0.162559 1
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT 5193 0.241768 1
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA 5402 0.235562 1
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA 5220 0.238969 1
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC 5063 0.205602 1
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC 5507 0.217041 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG 0.817559 7109 54911
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT 0.712516 6045 58271
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA 0.747220 6294 57101
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA 0.696659 7280 58238
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC 0.824061 7367 54121
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC 0.777599 6409 55400
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG 99804 37784 0.000000
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT 99790 35474 0.000000
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA 99768 36373 0.000000
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA 98810 33292 0.703254
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC 98720 37232 0.000000
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC 98479 36670 0.000000
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG 0.866667 0.0240722
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT 1.233333 0.0260196
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA 1.183333 0.0270728
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA 1.666667 0.0264143
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC 0.866667 0.0256432
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC 0.566667 0.0279603
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC SEA2253A58 2022-02-15
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC Mouse01-10 0.134247 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG Mouse DorsalHorn C10
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT Mouse DorsalHorn C10
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA Mouse DorsalHorn C10
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA Mouse DorsalHorn C10
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC Mouse DorsalHorn C10
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC Mouse DorsalHorn C10
ClustersH200
<character>
Mouse_DH_SEA2253A58#CGACAAAAAAAAAAAG C10
Mouse_DH_SEA2253A58#CAGTAAAAAAAAAAAT C10
Mouse_DH_SEA2253A58#CTGCAAAAAAAAAAAA C10
Mouse_DH_SEA2253A58#GTGTAAAAAAAAAAAA C10
Mouse_DH_SEA2253A58#GGGTAAAAAAAAAAAC C10
Mouse_DH_SEA2253A58#TTGGAAAAAAAAAAAC C10
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersH200", embedding = "UMAPH200")
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Biological.rep", embedding = "UMAPH200")
ggAlignPlots(p1, p3, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980049e08497-Date-2022-08-16_Time-12-03-18.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980049e08497-Date-2022-08-16_Time-12-03-18.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-198005396bdee-Date-2022-08-16_Time-12-03-33.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-198005396bdee-Date-2022-08-16_Time-12-03-33.log
# plot the confusion matrix of cell types by subjects
cM <- confusionMatrix(paste0(proj$ClustersH200), paste0(proj$Sample))
cM <- cM / Matrix::colSums(cM)
p <- pheatmap::pheatmap(
mat = as.matrix(cM),
color = paletteContinuous("whiteBlue"),
border_color = "black")
p
proj <- addImputeWeights(proj,
reducedDims = "HarmonyI200")
ArchR logging to : ArchRLogs/ArchR-addImputeWeights-198002fc4451d-Date-2022-08-16_Time-12-05-32.log If there is an issue, please report to github with logFile! 2022-08-16 12:05:34 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
## Neuron vs. Glia markers
markerGenes1 <- c('SRRM3',#Neurons
'MYT1L',#Neurons
'RBFOX3'#Neurons
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980044774358-Date-2022-08-16_Time-12-10-46.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:10:47 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980044774358-Date-2022-08-16_Time-12-10-46.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('ITGB4',#Astrocyte1
'GFAP',#Astrocyte1
'SLC7A10',#Astrocyte2
'PDZRN4'#Astrocyte2
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980063f21b71-Date-2022-08-16_Time-12-19-01.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:19:02 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980063f21b71-Date-2022-08-16_Time-12-19-01.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('RFX2'#Ependymal
# 'DNAH12'#Ependymal
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980013fe27a8-Date-2022-08-17_Time-13-55-42.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-17 13:55:54 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980013fe27a8-Date-2022-08-17_Time-13-55-42.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Error in x + guides(color = FALSE, fill = FALSE): non-numeric argument to binary operator
Traceback:
1. lapply(p, function(x) {
. x + guides(color = FALSE, fill = FALSE) + theme_ArchR(baseSize = 6.5) +
. theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) + theme(axis.text.x = element_blank(),
. axis.ticks.x = element_blank(), axis.text.y = element_blank(),
. axis.ticks.y = element_blank())
. })
2. lapply(p, function(x) {
. x + guides(color = FALSE, fill = FALSE) + theme_ArchR(baseSize = 6.5) +
. theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) + theme(axis.text.x = element_blank(),
. axis.ticks.x = element_blank(), axis.text.y = element_blank(),
. axis.ticks.y = element_blank())
. })
3. FUN(X[[i]], ...)
## Neuron vs. Glia markers
markerGenes1 <- c('LAMA2',#Meninges
'BICC1'#Meninges
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-198006ea1881c-Date-2022-08-16_Time-12-24-31.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:24:31 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-198006ea1881c-Date-2022-08-16_Time-12-24-31.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('MYO1F',#Microglia
'PALD1' #Microglia
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980033d588ae-Date-2022-08-16_Time-12-27-50.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:27:57 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980033d588ae-Date-2022-08-16_Time-12-27-50.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('QDPR',#Oligo1
'DPY19L1'#Oligo2
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-198001ef8d2e0-Date-2022-08-16_Time-12-31-19.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:31:21 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-198001ef8d2e0-Date-2022-08-16_Time-12-31-19.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('MEGF11',#OPC
'TNR'#OPC
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-198005ca021df-Date-2022-08-16_Time-12-34-45.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:34:49 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-198005ca021df-Date-2022-08-16_Time-12-34-45.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Neuron vs. Glia markers
markerGenes1 <- c('MPZ',#Schwann
'PMP22'#Schwann
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-198006462c53c-Date-2022-08-16_Time-12-38-19.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:38:22 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-198006462c53c-Date-2022-08-16_Time-12-38-19.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Excitatory vs. Inhibitory markers
markerGenes1 <- c('SLC17A6','FSTL4', # Excitatory
'SLC32A1','PAX2' # Inhibitory
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-198004699e154-Date-2022-08-16_Time-12-41-59.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 12:42:11 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-198004699e154-Date-2022-08-16_Time-12-41-59.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Marker Genes for differentiation of Excitatory Neurons
markerGenes1 <- c('GFRA1',
'CRHR2',
'COL13A1',
'NMUR2',
# 'TAC3',
'NMU',
'COL5A2',
'GHR',
'COL24A1',
'NMBR',
'TAC1',
# 'ANOS1',
'FSTL4',
'ADARB2',
'MAF',
'ST8SIA6',
'MAFA',
'NTNG1',
'ADAMTS16',
'TLL2',
'OTOGL'
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980050588545-Date-2022-08-16_Time-13-31-16.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 13:31:16 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980050588545-Date-2022-08-16_Time-13-31-16.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Marker Genes for differentiation of Inhibitory Nuerons
markerGenes1 <- c('MASP1',
'RREB1',
'NPY',
'MET',
'PTN',
'PDYN'
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-19800358307fa-Date-2022-08-16_Time-13-40-20.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-08-16 13:40:39 : Imputing Matrix Using weights on disk Using weights on disk Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-19800358307fa-Date-2022-08-16_Time-13-40-20.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## make UMAP plots of
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersH200", embedding = "UMAPH200")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAPH200")
ggAlignPlots(p1, p2, type = "h")
proj$logNFrags = log10(proj$nFrags)
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "logNFrags", embedding = "UMAPH200")
ggAlignPlots(p1, p3, type = "h")
p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "TSSEnrichment", embedding = "UMAPH200")
ggAlignPlots(p1, p4, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-198006e9f69b0-Date-2022-08-17_Time-11-22-16.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-198006e9f69b0-Date-2022-08-17_Time-11-22-16.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-19800793a7879-Date-2022-08-17_Time-11-22-26.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-19800793a7879-Date-2022-08-17_Time-11-22-26.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980075df092d-Date-2022-08-17_Time-11-22-34.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980075df092d-Date-2022-08-17_Time-11-22-34.log
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980029908a7f-Date-2022-08-17_Time-11-22-48.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980029908a7f-Date-2022-08-17_Time-11-22-48.log
############################################
# using marker gene scores, give cluster names
remapClust <- c(
'C1'='Micro',
'C2'='Drop',
'C3'='Drop',
'C4'='INH',
'C5'='INH',
'C6'='INH',
'C7'='INH',
'C8'='EXC',
'C9'='Drop',
'C10'='Drop',
'C11'='EXC',
'C12'='EXC',
'C13'='EXC',
'C14'='EXC',
'C15'='EXC',
'C16'='EXC',
'C17'='Schwann',
'C18'='Drop',
'C19'='Meninges',
'C20'='Micro',
'C21'='Astrocyte',
'C22'='Astrocyte',
'C23'='Schwann',
'C24'='Oligo',
'C25'='OPC'
)
proj$Celltype1 <- mapLabels(proj$ClustersH200, newLabels = remapClust,
oldLabels = names(remapClust))
table(proj$Celltype1)
Astrocyte Drop EXC INH Meninges Micro Oligo OPC
13816 13947 31882 7177 603 3472 33537 1408
Schwann
4263
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "Celltype1", embedding = "UMAPH200")
p1
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-1980037ddd101-Date-2022-08-17_Time-14-36-36.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-1980037ddd101-Date-2022-08-17_Time-14-36-36.log
# drop the drop clusters, pull out the neuron cell types
ARCHDIR2=file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_neuron')
neuronType = c( 'INH','EXC')
idxSample <- BiocGenerics::which(proj$Celltype1 %in% neuronType )
table(proj$Celltype1[idxSample])
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj, cells = cellsSample,
outputDirectory = ARCHDIR2, force = TRUE
)
EXC INH 31882 7177
Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!
Copying ArchRProject to new outputDirectory : /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_neuron
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 3): Embeddings
Copying Other Files (2 of 3): IterativeLSI200
Copying Other Files (3 of 3): IterativeLSI30
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# drop the drop clusters, pull out the glia cell types
ARCHDIR2=file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_glia')
idxSample <- BiocGenerics::which(proj$Celltype1 %ni% c(neuronType, 'Drop'))
table(proj$Celltype1[idxSample])
cellsSample <- proj$cellNames[idxSample]
proj2 = subsetArchRProject(
ArchRProj = proj,
cells = cellsSample,
outputDirectory = ARCHDIR2, force = TRUE
)
Astrocyte Meninges Micro Oligo OPC Schwann
13816 603 3472 33537 1408 4263
Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!
Copying ArchRProject to new outputDirectory : /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_glia
Copying Arrow Files...
Getting ImputeWeights
No imputeWeights found, returning NULL
Copying Other Files...
Copying Other Files (1 of 3): Embeddings
Copying Other Files (2 of 3): IterativeLSI200
Copying Other Files (3 of 3): IterativeLSI30
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
proj = saveArchRProject(ArchRProj = proj)
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|